Bonnie: aim to get a truth of diagnosis. Getting tumor tissue is paramount as well as properly preserved tissue. They use deep RNA sequencing and machine learning in their clinically approved tests.

Kevin: Serial biospace entrepreneur. Two diseases, cancer and neurologic, have been diseases which have been hardest to get reproducible and validated biomarkers of early disease. He concentrates on protein biomarkers.

Heather: FDA has recently approved drugs for early disease intervention. However the use of biomarkers can go beyond patient stratification in clinical trials.

Kevin: 15 approved drugs for MS but the markers are scans looking for brain atrophy which is too late of an endpoint. So we need biomarkers of early disease progression. We can use those early biomarkers of disease progression so pharma can target those early biomarkers and or use those early biomarkers of disease progression for endpoint

Bonnie: exciting time in the early diagnostics field. She prefers transcriptomics to DNA based methods such as WES or WGS (whole exome or whole genome sequencing). It was critical to show data on the cost savings imparted by their transcriptomic based thryoid cancer diagnostic test for payers to consider this test eligible for reimbursement.

Kevin: There has been 20 million CAT scans for cancer but it is estimated 90% of these scans led to misdiagnosis. Biomarker development has revolutionized diagnostics in this disease area. They have developed a breakthrough panel of ten protein biomarkers in serum which he estimates may replace 5 million mammograms.

All panelists agreed on the importance of regulatory compliance and the focus of new research should be on early detection. In addition they believe that Dr. Gotlieb’s appointment to the FDA is a positive for the biomarker development field, as Dr. Gotlieb understands the potential and importance of early detection and prevention of disease. Kevin also felt Dr. Gotlieb understands the importance of incorporating biomarkers as endpoints in clinical trials. Over 750 phase 1,2, and 3 clinical trials use biomarker endpoints but the pharma companies still need to prove the biomarkers clinical relevance to the FDA.They also agreed it would be helpful to involve advocacy groups in putting more pressure on the healthcare providers and policy makers on this importance of diagnostics as a preventative measure.

In addition, the discovery and use of biomarkers as disease endpoints has led to a resurgence of Alzheimer’s disease drug development by companies which have previously given up on these type of neurodegenerative diseases.

Kevin feels proteomics offers great advantages over DNA-based diagnostics, especially in cancer such as ovarian cancer, where a high degree of specificity for a diagnostic test is required to ascertain if a woman should undergo prophylactic oophorectomy. He suggests that a new blood-based protein biomarker panel is being developed for early detection of some forms of ovarian cancer.

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Please see related articles on Live Coverage of Previous Meetings on this Open Access Journal

University of Liverpool Scientists Report New Urine Test To Detect Potential Biomarkers of Prostate Cancer

A research team from the University of Liverpool has reached an important milestone towards creating a urine diagnostic test for prostate cancer that could mean that invasive diagnostic procedures that men currently undergo eventually become a thing of the past.

‘The use of a gas chromatography (GC)-sensor system combined with advanced statistical methods towards the diagnosis of urological malignancies’, published today in the Journal of Breath Research, describes a diagnostic test using a special tool to ‘smell’ the cancer in men’s urine.

Working in collaboration with the University of the West of England’s (UWE Bristol) Urological Institute team at Southmead Hospital and Bristol Royal Infirmary, the pilot study included 155 men presenting to urology clinics. Of this group, 58 were diagnosed with prostate cancer, 24 with bladder cancer and 73 with haematuria or poor stream without cancer. The results of the pilot study using the GC sensor system indicate that it is able to successfully identify different patterns of volatile compounds that allow classification of urine samples from patients with urological cancers.

Urgent need for earlier diagnosis

Professor Chris Probert from the University of Liverpool’s Institute of Translational Medicine began work on this project with UWE Bristol when he was working in Bristol as a gastroenterologist with clinical and research interest in inflammatory bowel disease.

The research team used a gas chromatography sensor system called Odoreader that was developed by a team led by Professor Probert and Professor Norman Ratcliffe at UWE Bristol. The test involves inserting urine samples into the Odoreader that are then measured using algorithms developed by the research team at the University of Liverpool and UWE Bristol.

Professor Probert said: “There is an urgent need to identify these cancers at an earlier stage when they are more treatable as the earlier a person is diagnosed the better. After further sample testing the next step is to take this technology and put it into a user friendly format. With help from industry partners we will be able to further develop the Odoreader, which will enable it to be used where it is needed most; at a patient’s bedside, in a doctor’s surgery, in a clinic or Walk In Centre, providing fast, inexpensive, accurate results.”

Like an electronic nose

Professor Norman Ratcliffe said, “There is currently no accurate test for prostate cancer, the vagaries of the PSA test indicators can sometimes result in unnecessary biopsies, resulting in psychological toll, risk of infection from the procedure and even sometimes missing cancer cases. Our aim is to create a test that avoids this procedure at initial diagnosis by detecting cancer in a non-invasive way by smelling the disease in men’s urine. A few years ago we did similar work to detect bladder cancer following a discovery that dogs could sniff out cancer. We have been using the Odoreader, which is like an electronic nose to sense the cancer.”

“The Odoreader has a 30 metre column that enables the compounds in the urine to travel through at different rates thus breaking the sample into a readable format. This is then translated into an algorithm enabling detection of cancer by reading the patterns presented. The positioning of the prostate gland which is very close to the bladder gives the urine profile a different algorithm if the man has cancer.”

Mr Raj Prasad, Consultant Urologist at Southmead Hospital, North Bristol NHS Trust, said: “If this test succeeds at full medical trial it will revolutionise diagnostics. Even with detailed template biopsies there is a risk that we may fail to detect prostate cancer in some cases. Currently indicators such as diagnosed prostatomegaly (enlarged prostate) and unusually high PSA levels can lead to recommendations for biopsy if there is a concern that cancer may be prevalent. An accurate urine test would mean that many men who currently undergo prostate biopsy may not need to do so.”

A link to the research article in the Journal of Breath Research is given below:

Abstract

Prostate cancer is one of the most common cancers. Serum prostate-specific antigen (PSA) is used to aid the selection of men undergoing biopsies. Its use remains controversial. We propose a GC-sensor algorithm system for classifying urine samples from patients with urological symptoms. This pilot study includes 155 men presenting to urology clinics, 58 were diagnosed with prostate cancer, 24 with bladder cancer and 73 with haematuria and or poor stream, without cancer. Principal component analysis (PCA) was applied to assess the discrimination achieved, while linear discriminant analysis (LDA) and support vector machine (SVM) were used as statistical models for sample classification. Leave-one-out cross-validation (LOOCV), repeated 10-fold cross-validation (10FoldCV), repeated double cross-validation (DoubleCV) and Monte Carlo permutations were applied to assess performance.

Significant separation was found between prostate cancer and control samples, bladder cancer and controls and between bladder and prostate cancer samples. For prostate cancer diagnosis, the GC/SVM system classified samples with 95% sensitivity and 96% specificity after LOOCV. For bladder cancer diagnosis, the SVM reported 96% sensitivity and 100% specificity after LOOCV, while the DoubleCV reported 87% sensitivity and 99% specificity, with SVM showing 78% and 98% sensitivity between prostate and bladder cancer samples. Evaluation of the results of the Monte Carlo permutation of class labels obtained chance-like accuracy values around 50% suggesting the observed results for bladder cancer and prostate cancer detection are not due to over fitting.

The results of the pilot study presented here indicate that the GC system is able to successfully identify patterns that allow classification of urine samples from patients with urological cancers. An accurate diagnosis based on urine samples would reduce the number of negative prostate biopsies performed, and the frequency of surveillance cystoscopy for bladder cancer patients. Larger cohort studies are planned to investigate the potential of this system. Future work may lead to non-invasive breath analyses for diagnosing urological conditions.

Other articles in this Open Access Journal related to Cancer Detection Systems include:

Outstanding Achievement in Pathology

Melville, Ny—Tracey Corey Handy, M.D., Chief Medical Examiner of Kentucky, and Matthew Zarka, M.D., affiliated with the University of Vermont and the Fletcher Allen Health Center, were recognized as the 1999 winners of the “Unsung Heroes” Awards. The awards, sponsored by Olympus America Inc., a world leading manufacturer of microscopes, in cooperation with the College of American Pathologists (CAP), were presented at a ceremony during the Fall CAP Conference in New Orleans.

The awards are the first in the on-going “Unsung Heroes” program sponsored by Olympus for the purpose of increasing public awareness of the vital and often invisible role pathologists have in saving lives. In addition to their expertise with a microscope, pathologists are the doctors who ensure that clinical laboratory testing is reliable and that diseases are accurately diagnosed. They are on the front lines whenever the public is threatened with disease. Their role in forensic science is crucial in helping prevent people from falling prey to abuse or avoidable illness. As Dan Biondi, Olympus Senior Vice President, points out, “Olympus is committed to supporting the work of the world’s pathologists and to advocating an educated patient population.”

Dr. Tracey Corey Handy is recognized as an “Unsung Hero” for her role in upgrading the well-being of children as Kentucky’s Chief Medical Examiner. Along with several colleagues, Dr. Handy founded the state’s “Living Forensics” team in 1991. Since its inception, the team has consulted on more than 700 cases of suspected child abuse. This effort has led to an increased conviction rate of abuse perpetrators and helps to reduce further cases of child abuse. In addition, Dr. Handy has initiated a program of routine screening for metabolic defects apparent in victims of Sudden Infant Death Syndrome (SIDS), which has resulted in the correct diagnosis of conditions that would have otherwise been attributed to SIDS. Dr. Handy has also chaired the state’s first child mortality review group that has resulted in the initiation of prevention programs, particularly in the event of accidental child death. A frequent speaker and contributor of her expertise to organizations throughout the country, she also teaches forensic pathology and has been published in more than a dozen peer-reviewed journals and books.

Dr. Matthew Zarka is recognized as an “Unsung Hero” for his efforts in aiding the extremely poor Mexican-Indian population in the remote mountain regions of Oaxaca, Mexico. Over the last two years Dr. Zarka has volunteered his time and services to bring much needed medical care to these impoverished communities. He and his OB/GYN team have been setting up the very first clinics throughout the area, enjoining the coffee companies of Mexico to spread word of the clinics to the local population and to help transport patients to the clinics. After each female patient underwent a gynecological examination, Dr. Zarka stained and read her Pap test. When needed, more extensive evaluations, biopsies, treatment and counsel were provided. Overwhelmingly successful, Dr. Zarka’s outreaching medical mission has grown to include additional professional staff. By volunteering his time and expertise, Dr. Zarka provides the only real access most people of the region have to modern medical care. His contribution has undoubtedly saved lives that might otherwise have been lost.

Stanford University

Benjamin Pinsky, MD, PhD, Assistant Professor of Pathology and Medicine (Infectious Diseases) is the recipient of the 2014 Siemens Healhcare Diagnostics Young Investigator Award. This award “honors outstanding laboratory research in clinical microbiology or antimicrobial agents and is intended to further the career development of a young clinical scientist and promote awareness of clinical microbiology as a career.”

Stephen J. Galli, MD, Chair of Pathology, Professor of Pathology and Microbiology and Immunology, and the Mary Hewitt Loveless, MD Professor, is the recipient of the 2014 ASIP (American Society of Investigative Pathology) Rouse Whipple Award. This award is presented to a senior scientist with a distinguished career in research who has advanced the understanding of disease and has continued productivity at the time of this award.

Dr. Raffick Bowen, Clinical Associate Professor and Associate Medical Director of SHC’s Clinical Chemistry and Immunology Laboratory is the recipient of the American Association of Clinical Chemistry’s Outstanding Speaker Award for 2013. This award recognizes his achievement in earning a speaker evaluation rating of 4.5 or higher during a 2013 continuing education activity accredited by AACC. The title of Dr. Bowen’s presentation is “Implementation of Autoverification in a Clinical Chemistry Laboratory: Theory to Practice”

Richard Kempson, MD,

Emeritus Professor of Pathology, is the recipient of the 2014 United States and Canadian Academy of Pathology (USCAP) President’s Award. The USCAP President’s Award is given annually to recognize an individual for outstanding service to the field of pathology.

Dr. Kempson is richly deserving of this award. Dr. Kempson has not only contributed substantially to the surgical pathology literature, particularly in gynecologic and soft tissue pathology but also, with Dr. Ronald Dorfman, he trained a substantial percentage of this and the next generation’s academic and community leaders in surgical pathology.

Dr. Kempson’s affiliation with Stanford University began in 1968 when he and Dr. Ronald Dorfman were recruited to Stanford to develop a program in surgical pathology. In short order, they established an internationally recognized residency and clinical fellowship program which went on to train more than 275 pathologists in the art and science of diagnostic surgical pathology. Dr. Kempson developed a distinctive teaching style that emphasized precise diagnostic criteria, approaching diagnosis with a broad morphologic differential diagnosis, and most importantly, always highlighting the relevance to patient management of the morphologic distinctions being made.

Prior to his recruitment to Stanford, Dr. Kempson was an Assistant Professor of Pathology and Surgical Pathology at Washington University. Dr. Kempson served as an Associate Professor of Pathology at Stanford from 1968 to 1974 and a Professor of Pathology from 1974 to 2001. In addition to his academic duties, he served as Co-Director of Surgical Pathology from 1968 until 2001. He also has served as President of the Association of Directors of Surgical Pathology (1993-1995), the United States and Canadian Academy of Pathology (1996) and the Arthur Purdy Stout Society (1996) and the California Society of Pathologists. The Richard Kempson, MD, Professorship in Surgical Pathology was established by the Department of Pathology in 2002 to honor him and his remarkable contributions to surgical pathology.

University of California, San Diego

A new era in diagnostics has emerged within the concept of Personalized Medicine. Imagine selecting cancer chemotherapy drugs based on knowledge of the precise mutations in a cancer. Can we predict who may have an adverse response to a medication based on that individual’s genetic blueprint? At UCSD, we are dedicated to making these resources available to our patients in the very near future. This is why we recently established the Pathology Center for Personalized Medicine. The goal of the Center is to conduct leading research necessary to form the foundation for advanced personalized medicine diagnostic testing and then to make this testing available in the CALM. For more information on the Center for Personalized Medicine, click here.

The research enterprise in Pathology at UCSD has grown dramatically in the past five years, and we are now amongst the top 15 programs in the country. Basic and translational research laboratories in the UCSD Pathology Department tackle important problems concerning cancer development and progression, angiogenesis, stem cell biology, neurodegenerative diseases, peripheral neuropathy, inflammation, infectious diseases, and wound healing. Our laboratories provide excellent environments for learning cell biology, molecular genetics, biochemistry, and animal physiology. Our faculty includes many active participants in the Biomedical Sciences (BMS) Graduate Program. For more information on this program, click here. We also have excellent opportunities for postdoctoral researchers. Please click here to visit our web page on summarizing the Pathology Department research enterprise. Then visit individual web pages for each of our faculty member to view specific research interests.

The Department of Pathology is home to both an outstanding Comparative Pathology and Medicine Program (for more information, click here) and the UCSD Research Ethics Program. We provide major educational support to the School of Medicine and the Skaggs School of Pharmacy and Pharmaceutical Sciences. For further information on these training opportunities, click here.

The La Jolla/San Diego community is a fertile environment for research and the pharmaceutical industry. The Sanford Burnham Medical Research Institute, the Scripps Research Institute, the Sidney Kimmel Cancer Center, the Salk Institute for Biological Studies, and the La Jolla Institute for Allergy and Immunology house exciting scientific programs and provide for numerous scientific collaborations. We also boast a plethora of biotechnology companies, located nearby on the La Jolla mesa.

The overall theme and focus of the Department of Pathology is to elucidate the molecular basis and pathology of human disease. The faculty is comprised of basic, translational and physician scientists that utilize the latest techniques in genomics, proteomics, cell biology, molecular biology and physiology to develop new diagnostic and therapeutic approaches for a wide range of diseases, including cancer, neurological disease, microbial infection, and inflammatory disease.

Steven L. Gonias, M.D., Ph.D.

Our laboratory is interested in identifying and characterizing novel pathways by which proteases and their cell-surface receptors regulate cell physiology. We are particularly interested in the function of proteases in cancer but also have active projects related to peripheral nerve injury, Alzheimer’s disease and cardiovascular biology. One focus involves urokinase-type plasminogen activator (uPA), a serine protease and plasminogen activator that binds with high affinity to a GPI-anchored receptor called uPAR. This event activates multiple cell-signaling pathways that affect cell migration, survival, and phenotype. We are actively working to elucidate mechanisms by which uPAR-initiated cell-signaling promotes cancer metastasis. We are particularly interested in breast cancer, but also work on prostate cancer and cancers of the central nervous system.

The complex of uPA with its inhibitor, PAI-1, is a ligand for a receptor called LRP-1. LRP-1 also is the receptor for other ligands, including extracellular matrix proteins, growth factors and foreign toxins. Our laboratory elucidated a pathway in which LRP-1 regulates cell-signaling indirectly, by regulating the cell-surface level of uPAR. However, recent studies suggest that LRP-1 also directly regulates cell-signaling by binding adaptor proteins, such as Shc and JIP. By this mechanism, LRP-1 regulates cell survival and gene transcription. Our current re­search is aimed at determining the role of LRP-1 in cancer and peripheral nerve injury, using in vitro and in vivomodel systems. Using proteomics approaches, we also are actively investigating the ability of LRP-1 to model the composition of the plasma membrane.

Our third area of focus concerns the plasma protease inhibitor, alpha2M. Our laboratory has demonstrated that this protein functions as a conformation-dependent carrier of growth factors. Alpha2M may also function in cell-signaling by binding to LRP-1. By site-directed mutagenesis, we have iso­lated and individually modified various functional sites in this multifunc­tional protein.

David Bailey, MD, PhD

David N. Bailey received his Bachelor of Science degree in Chemistry “with high distinction” from Indiana University and his Doctor of Medicine degree from Yale University. He completed a National Institutes of Health postdoctoral fellowship in Laboratory Medicine and a residency in Clinical Pathology, both at Yale, serving as Chief Resident in his final year. He is certified in Clinical Pathology and Chemical Pathology by the American Board of Pathology.

Dr. Bailey joined the University of California (UC) San Diego faculty in 1977 and served as Director of the Toxicology Laboratory of UC San Diego Medical Center (1977-2007), Head of the Division of Laboratory Medicine (1983-1989, 1994-1998), Acting Chair (1986-1988) and permanent Chair of the Department of Pathology (1988-2001), Director of the Pathology Residency Program (1986-1999), Director of Clinical Laboratories of UCSD Medical Center (1982-1999), Interim Vice Chancellor for Health Sciences and Dean of the UC San Diego School of Medicine (1999-2000 and 2006-2007), Deputy Vice Chancellor for Health Sciences (2001-2007), and Dean for Faculty & Student Matters in UC San Diego School of Medicine (2003-2007). From 2007 to 2009, he was Vice Chancellor for Health Affairs, Dean of the School of Medicine, and Professor of Pathology and Laboratory Medicine at the University of California, Irvine.

Dr. Bailey was recognized by the Institute of Scientific Information as one of the world’s ten most cited authors in forensic sciences (1981-93). He received the Gerald T. Evans Award from the Academy of Clinical Laboratory Physicians and Scientists in 1993 for his leadership and service to the Academy. Dr. Bailey has served as President of the California Association of Toxicologists (1981-1982), President of the Academy of Clinical Laboratory Physicians and Scientists (1988-89), and Secretary-Treasurer of the Association of Pathology Chairs (1996-99). He has also served on the Chemical Pathology Test Development and Advisory Committee of the American Board of Pathology; the Editorial Boards of Clinical Chemistry, the Journal of Analytical Toxicology, and the American Journal of Clinical Pathology; the Doris A. Howell Foundation for Women’s Health Research Board of Directors; the Board of Directors of the George G. Glenner Alzheimer’s Family Centers, Inc.; the Board of Directors of the Children’s Hospital of Orange County; the Board of Directors of Children’s Healthcare of California; the Board of Directors of the Rady Children’s Hospital of San Diego; the Board of Directors of the Veterans Medical Research Foundation (San Diego); and the Executive Committee and Governing Board of the California Institute of Telecommunications and Information Technology, among others.

David A. Herold, M.D., Ph.D.

My laboratory research interests are in the area of mass spectrometry application to clinical diagnostics. This includes prostaglandins, trace metal and steroids. Additionally, we has been involved in the development and validation of “classical” clinical chemistry diagnostic tests. The application of the mass spectrometry to determine the validity of endocrine tests, in particular testosterone, has been of particular interest. We have been using GC-MS, LC-MS, and MS-MS techniques for these investigations. At the present time, we are involved with the use of Accelerator Mass Spectrometry for the determination of calcium flux in serum and urine using 41Ca as a marker. The purpose of these studies is to better understand bone remodeling in normal and diseased patients. We have also investigated the use of microfluidics for the application to clinical diagnostics to measure selected proteins in a rapid and accurate manner.

The Cheresh laboratory focuses on the discovery of molecular pathways involved in the progression of cancer. Cheresh’s earlier work identified integrin αυβ3 as a biomarker of tumor angiogenesis and tumor progression, and was involved in the discovery of a drug called cilentigide which targets integrins αυβ3 and αυβ5.

The Cheresh laboratory has identified a series of critical microRNAs that regulate the growth of blood vessels. These microRNAs control the angiogenic switch that occurs during the earliest stages of tumor growth and neovascularization in the retina. As such one of these microRNAs may have therapeutic application as it is capable of maintaining blood vessels in the quiescent state.

Cheresh and colleagues have identified integrin αυβ3 as a biomarker of tumor stem cells during intrinsic or acquired resistance of a wide range of tumors including: cancer of the lung, pancreas, breast, and colon. Cheresh and his lab discovered that αυβ3 expression is both necessary and sufficient to account for tumor stemness and drug resistance based on its ability to drive a molecular pathway regulating these processes. This has led to the development of new therapeutic strategies to resensitize patients to drugs such as erlotinib and lapatinib that target EGFR.

The Cheresh laboratory has identified RAF kinase as an important target involved in tumor growth and angiogenesis. They have developed a new drug design strategy to target RAF and other relevant kinases by designing allosteric inhibitors of these targets. This is based on the use of defined chemical scaffolds to dock into an allosteric pocket on these kinases to render them inactive. The combined use of in silico and biological screening has yielded drugs with nM anti-tumor activity that produce strong anti-tumor growth in mouse models following once a day oral dosing. This approach appears to yield drugs that target tumors that are resistant to ATP mimetic inhibitors of RAF, Kit or PDGFR

John Lowe

Senior Director, Pathology

I joined Genentech in 2008 as Senior Director of Pathology, after having spent more than 18 years as an HHMI Investigator at the University of Michigan and then 3 years as Chair of Pathology at Case Western Reserve University School of Medicine. The role of Senior Director of Pathology in Research at Genentech offered attractive opportunities to do research in an outstanding, disease-focused scientific environment, while also helping to lead the scientific and research support activities of the Pathology department. These latter efforts help Genentech continue to make a major positive difference to the health and well being of a large number of patients afflicted with cancer, autoimmune syndromes, neurodegenerative diseases and other illnesses for which therapies are unsatisfactory or nonexistent.

An exceptional team of pathologists, laboratory managers, scientific associates and administrative staff in the department collaborate with me in these efforts. Additional outstanding pathologists, scientists, and managers continue to be recruited to assist us in ensuring that the department performs at the highest level. Our task is made more straightforward by the environment at Genentech, which is characterized by exceptionally bright, motivated and collaborative colleagues at every level, spectacular facilities, and workplace philosophies that are conducive to the highest levels of achievement.

Postdoctoral Mentor

The opportunity to mentor postdoctoral fellows at Genentech has been a stimulating and gratifying experience for me. This derives in part from the freedom afforded by the program to pursue research directions that are deemed to be important and interesting, even if these have no immediate therapeutic relevance. The special mentoring experience also derives from extraordinary breadth and quality of the core laboratories at Genentech, and the spectacular intellectual environment. Together, these circumstances provide an unparalleled opportunity for postdoctoral fellows, and their mentors, to engage in biomedical discovery of the highest caliber.

Cancer Biomarkers [11.3.2.3]

Writer and Curator: Larry H. Bernstein, MD, FCAP

Cancer Biomarkers

This discussion is extracted from the Special Section – Cancer Biomarker Update – in May Arch Pathology and Lab Med. It is not intended to be complete, but it has quite timely content. There are three articles I shall cover.

11.3.2.3 Cancer Biomarkers

11.3.2.3.1 Cancer Biomarkers in Structured Data Reporting

11.3.2.3.2 Cancer Biomarkers in Myeloid Malignancies

11.3.2.3.3 National Comprehensive Cancer Network Consensus on Use of Cancer Biomarkers

The College of American Pathologists has been producing cancer protocols since 1986 to aid pathologists in the diagnosis and reporting of cancer cases. Many pathologists use the included cancer case summaries as templates for dictation/data entry into the final pathology report. These summaries are now available in a computer-readable format with structured data elements for interoperability, packaged as ‘‘electronic cancer checklists.’’ Most major vendors of anatomic pathology reporting software support this model. Objectives.—To outline the development and advantages of structured electronic cancer reporting using the electronic cancer checklist model, and to describe its extension to cancer biomarkers and other aspects of cancer reporting. Data Sources.—Peer-reviewed literature and internal records of the College of American Pathologists. Conclusions.—Accurate and usable cancer biomarker data reporting will increasingly depend on initial capture of this information as structured data. This process will support the standardization of data elements and biomarker terminology, enabling the meaningful use of these datasets by pathologists, clinicians, tumor registries, and patients.

Narrative Versus Structured Data Reporting Clinical laboratory reports typically consist of discrete data elements with structured qualitative or quantitative information, often using standardized laboratory methods, data elements, and units. When discrete data elements are electronically transmitted to external clinical information systems, the transmitted information may be annotated with one or more terminologies such as Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT)4 and Logical Observation Identiﬁers Names and Codes (LOINC),5 although the consistent application of such codes to structured laboratory data is not yet an interoperable standard. Because the structure of clinical laboratory data tends to be ﬁxed and standardized before the point of data entry, reporting these data elements in a tabular synoptic format is a relatively simple process. The report output may not include all data collected (eg, methodologic details), but clinically relevant data can be easily extracted by computer algorithm and automatically reported in easily readable format (including custom text, result explanations, and test value trends).

Anatomic pathology reports, by contrast, have traditionally been narrative and recorded as unstructured or partially structured ﬁelds of text. Unfortunately, narrative reporting often lacks consistency in organization, content, units, terminology, and completeness.6–8 These structural inconsistencies create difﬁculties in ﬁnding and understanding clinically important data and increase the chance of omitting key data elements and misinterpreting information present in the narrative. This is particularly problematic when clinicians encounter reports from multiple pathology laboratories or when patients receive care at multiple institutions. Narrative reporting has equally negative effects on computer readability; the ability of computers to correctly parse and classify information contained in a narrative report is imperfect even when using advanced natural language processing software designed speciﬁcally for anatomic pathology.9,10 Natural language processing–parsed text must always undergo human review, editing, and signoff before release for patient care or research.

Ensuring consistency and readability of cancer and biomarker reports requires a reporting solution integrated into the pathologist workﬂow that supports entry of standardized data directly into a laboratory information system and/or electronic health record system. These systems can produce highly readable synoptic reports and can include computer-based report validation of standardized data elements to reduce or eliminate the chance of omitting required data elements. With the transition from narrative to synoptic reporting for cancer cases, many laboratories have been using modiﬁed CCPs or locally developed templates or macros, which may or may not contain all required data elements. This common mode of data entry ﬁts well into the pathologist workﬂow and can result in organized, highly readable synoptic reports, but generally results in information stored as text in a single large data ﬁeld. Even when results are entered as discrete data elements, subsequent storage mechanisms usually result in nonstructured text or nonstandard custom data ﬁelds in a local computer system. Unfortunately, narrative and nonstandardized data sets are very difﬁcult to reliably aggregate and analyze for laboratory quality assurance, research, or cancer registry surveillance. Such aggregated data also remain relatively unreliable because of changes in information systems. Many of these issues can be eliminated by entering and reporting structured data with standardized electronic templates.

CAP eCC History, Development, and Adoption Efforts to bring structure to cancer pathology reporting began in the late 1980s and early 1990s1,11,12 with publication of templates that were the precursors of the current CCPs (Table). The primary goal was to improve the care of cancer patients by improving the reporting rate of clinically important data elements. The checklist approach was adopted to help standardize terminology and ensure all relevant data elements are reported. The 66 current CCPs, 3 new cancer biomarker templates,13–16 and 85 eCC templates represent the evolution of the original 1986 CCP model. The CCPs and templates are created and maintained through the ongoing work of the CAP Cancer and Cancer Biomarker Reporting Committees. The CCPs are widely adopted by laboratories and used for accreditation purposes by the American College of Surgeons–Commission on Cancer17 and CAP Laboratory Accreditation Program.18

During the past several years, the CAP has worked to create standardized pathology reporting templates that enable individual pathologists and software vendors to capture, store, retrieve, transmit, and analyze diagnostic cancer pathology information. Electronic versions of these templates, the eCCs, are based on consistent structured data representation, which enables simple yet robust computerization of cancer pathology data elements suitable for patient care, cancer registry transmission, and research. Synoptic reports are not the same as ‘‘structured data.’’ Although synoptic reports are formatted for optimum human readability and understanding, they consist of textbased questions and answers (ideally one pair per line) that present problems for computer readability and interoperability. Structured data, by contrast, refers to representation of data elements in a computer-readable data exchange format such as XML. The structured data model used by eCC XML templates assigns a unique identiﬁer (a composite key) to every question and answer choice, template, section, and note listed in the template. Composite keys are used throughout the entire eCC life cycle to transmit the precise identity of each data element and its origin in a speciﬁc version of an eCC template.

The CAP eCC model has been implemented province wide by Cancer Care Ontario through their multiyear synoptic pathology reporting and change-management project.19–21 The Canadian Partnership Against Cancer is also currently working with several other Canadian provinces to implement population-level electronic synoptic reporting based on the CAP eCC. The Cancer Care Ontario project has shown that there is high acceptability among pathologists and clinicians22 and that data are usable for the secondary needs of tumor registries,20 but there remains room for improvement. For instance, both the Reporting Pathology Protocols project reports23–25 and the Cancer Care Ontario implementation reports22 suggest that pathologists require more time to complete the reporting task.

While this may meet quality and data reporting needs, it remains a potential barrier to acceptance. Automated human-readable report generation also could be improved, especially in terms of creating best practice guidelines for report output. Both data entry and report generation have traditionally been supported by laboratory information systems vendors, but the success of implementation has varied, and often signiﬁcant effort is required to modify the resultant human readable report to satisfy local clinical needs. Because the ﬁnal report remains most important for patient care, the CAP Diagnostic Intelligence in Health Information Technology and Pathology Electronic Reporting committees have initiated work on creating and promoting a standardized data structure within cancer pathology reports.

2013 eCC-based reporting in Ontario is used to improve quality and practice performance.20

2013 The first cancer biomarker templates are produced for breast, colorectal, and lung cancer.13–16 They are available on the http://www.cap.org/cancerprotocols Web site in Word and PDF format (accessed April 28, 2014). The eCC versions are available through CAP.

2013 Launch of CAP eFRM, a software product to aid vendor integration of eCCs into AP-LIS systems or for use as a standalone product.

Figure 2. (not shown) The College of American Pathologists (CAP) Cancer Protocols (CCPs) are developed by the CAP Cancer Committee. Each CCP is reformulated as question/answer structures, entered into the CAP electronic Cancer Checklist (eCC) Template Editor (not shown), and stored in the eCC template database. The eCC files in XML format are produced from this database and delivered to vendors of anatomic pathology/laboratory information system (LIS) software systems. Vendors convert the eCC files into data entry form implementations using their local technologies. In addition, most vendors create eCC-based templates for creating synoptic reports. When pathologists enter data into the eCC-based data-entry forms, the vendor software is able to run validation checks such as assessing whether all CCP-required data elements are recorded. Synoptic reports are developed from the eCC-derived data and delivered to health care providers for patient care. The eCC-structured data is stored in the vendor database, where it can be transmitted in interoperable format to other computer systems. Secondary uses of eCC-based data include cancer registry reporting, quality assurance, biospecimen annotation, research, decision support, and financial reporting. The horizontal arrows involve the exchange of eCC composite keys, preserving the fidelity of the data as part of an eCC template, providing the foundation for interoperable data transmission formats, and enabling the regeneration of eCC datasets in the exact format in which they were recorded. Activity columns that directly impact health care activities are shaded in light blue. Abbreviation: EHR, electronic health record.

Future The use of standardized, structured data elements is foundational for the development of improved reporting and clinical decision support for biomarker results. Clinicians are currently faced with synthesizing data from multiple narrative reports to decide on treatment options. Often these narrative reports are from different laboratories with very different report formats and include variable methodologic details, all of which hinders understanding of important results. For biomarkers that determine a patient’s eligibility for speciﬁc drugs, a computer-generated report that presents test results in a tabular form, similar to antibiotic susceptibility testing, may be desirable. This reporting method would allow for display of biomarker test results over time and could also link to other databases.

Structured data allows for clinical decision support such that the report displays only eligible drugs, or the report displays a note stating that a test result suggests a patient is not eligible for a speciﬁc drug. Using standardized terminology allows these rules to be the same between institutions, even if electronic health record system vendors use different means of implementation.

This system would allow for more efﬁcient, more accurate, and safer methods of providing data for optimizing patient care, with all of the discrete data transmitted electronically and linked to the original tumor report. In Ontario, Canada, this vision is rapidly advancing, as demonstrated by the Cancer Care Ontario successes with eCC implementation and current plans to implement the eCC biomarker templates across the province. Future challenges include the identity and tracking of related tumor samples over time and integration of testing from different laboratories. Because testing on a given specimen can be performed at different times and in different laboratories, a future standard must address the annotation of results with tumor source, procurement dates, and other biospecimen-speciﬁc data.30 The relationship of test results from multiple specimens from the same patient needs to be recorded in a standard format so that this parent-child hierarchical relationship can be analyzed over time.

Pathologists are increasingly asked to provide biomarker information for patient care, tumor registries, epidemiologic studies, translational research, and quality improvement activities.20 The eCC model provides a pathway to meet these demands, with efﬁcient and error-free data entry, reporting, and transmission of data elements, and with the ability to produce output that is human readable, efﬁcient to use, and easy to interpret. As the CCPs and eCCs have matured, Ontario pathologists and cancer registries have demonstrated success with large-scale implementations. However, continued improvements are needed. As the ﬁeld of pathology grows, particularly in the area of biomarkers, structured electronic reporting will become critical to helping physicians provide optimal patient care and will facilitate secondary uses of pathology data.

Recent studies using massively parallel sequencing technologies, so-called next-generation sequencing, have uncovered numerous recurrent, single-gene variants or mutations across the spectrum of myeloid malignancies. Objectives.—To review the recent advances in the understanding of the molecular basis of myeloid neoplasms, including their significance for diagnostic and prognostic purposes and the possible implications for the development of novel therapeutic strategies. Data Sources.—Literature review. Conclusions.—The recurrent mutations found in myeloid malignancies fall into distinct functional categories.

These include (1) cell signaling factors, (2) transcription factors, (3) regulators of the cell cycle, (4) regulators of DNA methylation, (5) regulators of histone modification, (6) RNA-splicing factors, and (7) components of the cohesin complex. As the clinical significance of these mutations and mutation combinations is established, testing for their presence is likely to become a routine part of the diagnostic workup. This review will attempt to establish a framework for understanding these mutations in the context of myeloproliferative neoplasms, myelodysplastic syndromes, and acute myeloid leukemia.

Pathways Affected by Recurrent Mutations in Myeloid Malignancies

Cell Signaling The ability of a cell to respond to diverse physiologic stimuli, including cytokines, chemokines, growth factors, and hormones, or to the presence of bacteria and other microorganisms is mediated via the interaction of speciﬁc ligands and their corresponding cell surface receptors. Ligand binding usually results in receptor dimerization and activation of a tyrosine kinase, either intrinsically present in the cytoplasmic domain or as an associated polypeptide. Further propagation of the signal from the cell surface to the nucleus involves the formation of macromolecular complexes and the activation or inactivation of various enzymes. The ﬁnal outcome of the signal transduction is modulation of the expression of certain genes and their products, which ultimately produces a cellular response. In normal cells, this process is tightly regulated owing to the involvement of negative or inhibitory signals. In tumor cells these processes may be perturbed owing to mutations that impart inappropriate activation or deactivation of enzymatic function. Genes for receptor protein tyrosine kinases, such as FLT3 and KIT, or receptor-associated kinases, such as JAK2, are the most commonly mutated cell-signaling factors in myeloid malignancies. Activating mutations in these proteins occur in narrowly deﬁned hotspots, resulting in ligand-independent dimerization or constitutive kinase activation. An example is the protein tyrosine kinase JAK2, which transduces signals from ligand-bound cell surface receptors for thrombopoietin (TPOR/MPL) and erythropoietin (EPOR).

Activating mutations in JAK2 are commonly found in the myeloproliferative neoplasms (MPNs): polycythemia vera (PV), essential thrombocythemia (ET), and primary myeloﬁbrosis (PMF). These disorders appear to be driven, in large part, by the inappropriate activation of growth factor– signaling pathways, and JAK2 is central to signaling from EPOR and TPOR/MPL via STAT5, STAT3, the RAS-MAP kinase pathway, and the PI-3 kinase–AKT pathway. Many negative regulators of cytokine signaling, such as SH2B adaptor protein 3 (SH2B3, also known as LNK)1,2 and cytokine-inducible SH2-containing protein (CISH, also known as SOCS)3 keep the pathway in balance. Downstream RAS signaling is counteracted by NF1, a protein that stimulates the intrinsic RAS guanosine triphosphatase activity. An effect similar to JAK2 mutations may be achieved through mutations in other proteins involved in these pathways, including activating mutations of a surface receptor (MPL) or loss-of-function mutations in negative regulators (SH2B3, CISH), all of which promote survival, proliferation, and differentiation of committed myeloid progenitors.4 Example genes included in this group: JAK2, MPL, KIT, FLT3, CSF3R, PTPN11, KRAS, NRAS, and NF1.

Transcription Transcription is a tightly regulated process that depends on the formation and assembly of protein and protein-DNA complexes. These complexes, called transcription factors, bind to speciﬁc DNA sequences adjacent to the genes they regulate and promote (in the case of an activator) or block (in the case of a repressor) the recruitment of RNA polymerases to those genes. This regulatory activity controls the formation of messenger RNA (mRNA) transcripts. Mutations that block the activity of transcriptional activators may, in certain circumstances, lead to a block in cellular differentiation due to the lack of the necessary gene products. Many of the transcription factors that are recurrently mutated in myeloid malignancies, such as RUNX1, GATA1, GATA2, and CEBPA, are involved in fundamental aspects of myelopoiesis and it is believed that these mutations lead to a block in myeloid differentiation. Example genes included in this group: RUNX1, CEBPA, GATA1, GATA2, ETV6, and PHF6.

Epigenetic Modifiers: Regulation of DNA Methylation DNA methylation involves the addition of a methyl group to cytosine bases in the context of cytosine-guanine sequences (so-called CpG sites), leading to the creation of 5-methylcytosine. CpG islands are usually located in or near promoter regions. Their methylation is an important epigenetic mechanism for regulating gene expression and, in the context of heritable methylation patterns, underlies the process of genomic imprinting. Additionally, it has been hypothesized that aberrant DNA methylation may contribute to the pathogenesis of cancers,5–8 including myeloid neoplasms. Although cancer genomes tend to be globally hypomethylated, in comparison with normal tissues, hypermethylation of speciﬁc CpG islands at tumor suppressor genes, resulting in their inactivation, is common in many tumors.9

ormation of compact, inactive heterochromatin.10 Several factors regulate the process of DNA methylation. Mutations in some of these factors have been found recurrently in myeloid neoplasms.11–13 DNA methyltransferases catalyze the methylation at the 50 position of cytosine. DNMT3A and DNMT3B are involved in de novo methylation, whereas DNMT1 maintains hemimethylated DNA during replication. Once created, 5-methylcytosine can be further modiﬁed by a group of methylcytosine dioxygenases (Ten Eleven Translocation dioxygenases: TET1, TET2, and TET3) to 50-hydroxymethylcytosine, a presumed short-lived intermediary that may lead to demethylation of cytosine.

Mutations in both DNMT3A and TET2 likely lead to loss of function of the respective enzyme activities. Recently, mutations in IDH1 and IDH2 have been identiﬁed in myeloid neoplasms and other cancers. Interestingly, recurring mutations of an arginine residue in the active site (R132 in IDH1 and R140 in IDH2) prevent the normal catalytic function of the enzyme (conversion of isocitrate to aketoglutarate) and appear to induce a neomorphic enzyme activity resulting in the formation of the rare oncometabolite 2-hydroxyglutarate.14 TET2 belongs to a family of dioxygenases that requires a-ketoglutarate as a cofactor.15,16 It has been shown that 2-hyroxyglutarate acts as a competitive inhibitor of a-ketoglutarate–dependent dioxygenases, which include TET2 and members of the KDM family of histone demethylases, thereby inducing epigenetic changes at both the level of DNA methylation and histone modiﬁcation.14,17

Therapeutic inhibitors of mutant forms of IDH proteins and the resulting 2-hydroxyglutarate are also under investigation.18 Example genes included in this group: DNMT3A, TET2, IDH1, and IDH2.

Epigenetic Modifiers: Mutations Affecting Histone Function Histone proteins are involved in the dynamic organization of DNA into zones of active euchromatin and inactive heterochromatin in a process that is regulated, in part, by a complex series of posttranslational modiﬁcations to histone tails, including acetylation and methylation. These modiﬁcations affect the recruitment of regulatory proteins such as transcription factors, corepressors, and coactivators, as well as histone-modifying enzymes themselves. Trimethylation of the lysine at position 27 in histone H3 (H3K27), one of the more common modiﬁcations, generally leads to reduced gene expression and it would be expected that mutations that reduce methylation at H3K27 would activate transcription. Recently, recurrent mutations in several genes encoding histone regulators, including ASXL1, EZH2, SUZ12, and KDM6A (also known as UTX), have been identiﬁed.

Perturbations in epigenetic pathways result in global, genome-wide effects and it is often difﬁcult to identify which altered cellular function eventually leads to neoplasia. The same also holds true for perturbations in the RNA splicing machinery and the cohesion complex (see below). Example genes included in this group: ASXL1, EZH2, SUZ12, and KDM6A.

RNA-Splicing Factors RNA splicing results in the formation of mature mRNA transcripts derived from exons, the protein coding portion of the genome. Splicing occurs in a macromolecular complex of small nuclear RNAs and proteins assembled de novo on each pre-mRNA strand in a multistep process. This complex is known as the spliceosome. Transcripts may undergo alternative splicing in a tissue, or context-speciﬁc manner and the protein products of alternatively spliced transcripts may have altered function.
Example genes included in this group: SF3B1, SRSF2, ZRSR2, and U2AF1.

Cell Cycle Regulators Example genes included in this group: TP53 and NPM1.

Genetic Biomarkers in Myeloid Malignancies

Myeloproliferative Neoplasms Myeloproliferative neoplasms encompass a group of clonal stem cell disorders characterized by expansion of 1 or more of the myeloid lineages resulting in bone marrow hypercellularity and increased peripheral blood myeloid cell counts. The MPN category includes chronic myelogenous leukemia, PV, ET, PMF, chronic neutrophilic leukemia, mastocytosis, and others. The underlying genetic landscape of some of these disorders is very well understood, as in the case of chronic myelogenous leukemia with t(9;22), but is much less well understood in many other entities.

The discovery of a recurrent codon 617 activating mutation (V617F) in exon 14 of the tyrosine kinase JAK237–40 and additional mutations in JAK2 exon 1241 provided the ﬁrst genetic evidence of the importance of dysregulated growth factor signaling in these disorders. The prevalence of JAK2 mutations in classical MPNs varies from 95% to 99% in PV, 50% to 70% in ET, 40% to 50% in PMF,37–41,43 and molecular tests for their detection are available and widely used in clinical practice. Similarly, activating mutations in the MPL gene, encoding the thrombopoietin receptor, are present in approximately 4% of ET cases and approximately 11% of PMF cases.44–47 Recently, calreticulin (CALR), encoding an endoplasmic reticulum chaperone, has also been shown to be important. Somatic CALR mutations are found in 70% to 84% of patients with ET or PMF with wild-type JAK2 and MPL, 8% of MDS cases, and occasionally in other myeloid neoplasms.48 Clonal analyses suggest CALR mutations act as an initiating mutation in some patients.48 In ET and PMF, CALR mutations and JAK2 and MPL mutations are mutually exclusive,49 and CALR mutations appear to be absent in PV.49 CALR mutations appear to be primarily insertion or deletion mutations that result in a frameshift and the subsequent generation of a novel C-terminal peptide.48,49

Many other genes involved in intracellular signaling, such as negative regulators of the JAK2 signaling pathway, are mutated in MPNs. Among these is SH2B3, which negatively regulates JAK2 activation through its SH2 domain. Mutations in SH2B3 during the chronic phase are uncommon, fewer than 5% in ET and PMF50; however, their frequency increases during leukemic transformation, suggesting a role in disease progression.51 Another negative regulator found mutated in MPNs is the Cbl proto-oncogene, E3 ubiquitin protein ligase gene (CBL). CBL acts as a multifunctional adapter with ubiquitin ligase activity and by competitive blockade of signaling.

A shift from a simple, chronic myelogenous leukemia–like model for MPN pathophysiology to a more complex model occurred with the emergence of evidence of a ‘‘pre-JAK2’’ genetic event. This concept is based on the observation that mutations in signaling molecules are not sufﬁcient for disease development and that several cooperating genetic hits appear to be required.4 Mutations in genes involved in epigenetic regulation, including EZH2, ASXL1, and TET2 (also found in many other myeloid neoplasms), are postulated to act as those initialing events, preceding JAK2V617F mutations.55 EZH2 mutations do not occur in ET, but are present in 3% of PVs and 13% of MFs.56 ASXL1 mutations are found in only approximately 7% of patients with ET and PV but more frequently in PMF cases (from 19%–40%).57,58 TET2 mutations occur in approximately 14% of MPNs, ranging from 11% in ETs to 19% in PMFs.59,60 Finally, there are mutations that are rarely found during the chronic phase but which may be present at transformation, and are therefore thought to play a role in disease progression. IDH1 and IDH2 mutations, for example, have a low frequency in the chronic phase (0.8% in ET, 1.9% in PV, and 4.2% in MF) but a much higher frequency in blast phase.61

Myelodysplastic Syndromes and MDS/MPN Overlap Disorders

The myelodysplastic syndromes are a group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis, morphologic evidence of dysplasia in at least 1 of the myeloid lineages, peripheral cytopenias, bone marrow hypercellularity, and an increased risk of development of AML.74 Clonal cytogenetic abnormalities, including large deletions and chromosome gains, as well as balanced translocations, are observed in approximately 50% of MDS cases by routine methods,74 and their identiﬁcation aids in establishing the diagnosis and may provide prognostic information.

Acute Myelogenous Leukemia Acute myeloid leukemia is a genetically heterogeneous disease resulting in the accumulation of myeloblasts in bone marrow with a concomitant reduction in normal hematopoiesis. The diagnosis and subclassiﬁcation of AML depends on detecting the presence of recurrent cytogenetic abnormalities.74 In many cases, particularly those that are cytogenetically normal (CN-AML), several single-gene mutations further aid in the stratiﬁcation of disease outcomes. The signiﬁcance of mutations in genes such as FLT3, NPM1, and CEBPA is well established but nextgeneration sequencing has led to the discovery of numerous additional recurrent mutations, including in TET2,12,59 ASXL1,104 IDH1/IDH2,13,105,106 DNMT3A,11,107 and PHF6.108

Among the most common mutations found in de novo AML are NMP1, FLT3, and DNMT3A mutations, present in 22% to 29%, 22% to 37%, and 15% to 26% of samples, respectively.31,110,111 Other genes less commonly targeted by mutations are IDH1/IDH2 (15%– 20%), KRAS/NRAS (12% combined), RUNX1 (5%–10%),TET2 (8%–14%), TP53 (2%–8%), CEBPA (6%–14%), WT1 (6%–8%), PTPN11 (4%), and KIT (4%–6%).31,110,111

The prognostic signiﬁcance of a subset of recurrent mutations is well established. In CN-AML, biallelic CEBPA mutations127,128 and NPM1 mutations without FLT3-ITD mutations129–133 are associated with a favorable prognosis. In contrast, FLT3-ITD without NPM1 mutations112,113,129–132 and MLL–partial tandem duplication mutations134–136 portend poor outcome. KIT mutations in AML with t(8;21) or inv(16)131,137 are also associated with unfavorable outcome. The European LeukemiaNet panel138 ﬁrst proposed a standardized classiﬁcation according to both cytogenetic and molecular genetic data to allow a better comparison of prognosis among patients with AML. However, only mutations of NPM1, CEBPA, and FLT3 were included in their recommendations. The relevance of more recently discovered mutations, including IDH1, IDH2, WT1, TET2, ASXL1, among others, remains unclear.139–142 The presence of certain mutations may also allow for more targeted therapeutic regimens; for example, FLT kinase inhibitors may be useful in cases with mutations and IDH1 inhibitors are under investigation in patients with IDH1 mutations.143,144

An enormous amount of new information illuminating the genetic complexity of myeloid neoplasms has been generated during the last few years. Much work remains to be done but it is clear that the future role of the pathologist in collecting and interpreting this information will be an essential component of the management of these patients.

The rapid development of commercial biomarker tests for oncology indications has led to confusion about which tests are clinically indicated for oncology care. By consolidating biomarker testing information recommended within National Comprehensive Cancer Network Clinical Practice Guidelines in Oncology (NCCN Guidelines), the NCCN Biomarkers Compendium aims to ensure that patients have access to appropriate biomarker testing based on the evaluations and recommendations of the expert NCCN panel members.Objectives.—To present the recently launched NCCN Biomarkers Compendium. Data Sources.—Biomarker testing information recommended within NCCN Clinical Treatment Guidelines as well as published resources for genetic and biological information. Conclusions.—The NCCN Biomarkers Compendium is a continuously updated resource for clinicians who need access to relevant and succinct information about biomarker testing in oncology and is linked directly to the recommendations provided within the NCCN Clinical Practice Guidelines.

Most recommendations contained within the NCCN Guidelines are based upon lower-level evidence and uniform NCCN consensus (category 2A).1 This is not a deﬁciency of the guidelines, but is rather because high-level evidence is not available for most decisions across the continuum of care. A deeper look at what constitutes a ‘‘recommendation’’ might begin to clarify that issue. A recommendation can include all of the recommended workup, surgical options, options for chemotherapy, and tests recommended for ongoing surveillance. Although many of these options are routinely used as standard of care in clinical practice, there is often not the available body of high-level evidence that supports category 1 recommendations, thus most are category 2A levels of evidence and consensus. In other instances, recommendations for chemotherapy regimens for which there is high-level, randomized clinical trial evidence are listed as category 1.

Several derivative products arise from the NCCN Guidelines. The NCCN Drugs & Biologics Compendium (NCCN Compendium) is a resource outlining appropriate use of drugs and biologics as recommended in the NCCN Guidelines. To be included in the compendium, an agent must ﬁrst be recommended in at least 1 of the NCCN Guidelines. The compendium is typically used by clinicians and payors to determine appropriate use and as a standard to determine coverage. The rapid development and commercialization of biomarker and companion diagnostic testing in cancer gave rise to the NCCN Biomarkers Compendium, to be used by both payors and clinicians to facilitate identiﬁcation of biomarker tests recommended for use by NCCN guideline panels. The NCCN uses a broad deﬁnition of ‘‘biomarker’’ for the purposes of this compendium. All tests measuring genes or gene products, which are used for diagnosis, screening, monitoring, surveillance, or for providing predictive or prognostic information, are included in the biomarkers compendium. This compendium focuses on the biology of the biomarker itself and its clinical utility in supporting clinical decision making. Information is organized by the biomarker being measured, and not by listing of commercially available tests or test kits. Close to 1000 biomarker testing recommendations are included in the NCCN Biomarkers Compendium.

The NCCN Biomarkers Compendium is presented on the NCCN Web site as a series of drop-down menus, allowing users to pick from menus listing Guideline, Disease, Molecular Abnormality, or Gene Symbol.3 Users can retrieve all recommendations for a particular disease, or can select a gene-based search in order to show which diseases have a validated use for a particular gene test. Additional ﬁelds can be displayed by selecting from a series of boxes to the right of the drop-down menus (see Figure 1, which shows default ﬁelds for RAS testing in colon cancer). Once records are displayed, the resulting table can be sorted by the information in any of the displayed columns. If a searcher chooses, all records can be displayed and then searched with any text term or sorted by any of the columns for a more comprehensive picture of the contents of the database.

Figure 1. (not shown) KRAS mutation testing recommendation from the National Comprehensive Cancer Network (NCCN) Biomarkers Compendium.3 Reproduced with permission from the NCCN Biomarkers Compendium [1] 2014 National Comprehensive Cancer Network, Inc. (NCCN.org; accessed February 21, 2014). To view the most recent and complete version of the NCCN Biomarkers Compendium, go online to NCCN.org. National Comprehensive Cancer Network, NCCN, NCCN Guidelines, and all other NCCN content are trademarks owned by the National Comprehensive Cancer Network, Inc.

Disease Description

Colon cancer

Specific Indication

Metastatic disease

Molecular Abnormality

KRAS/NKRAS mutation

Test

KRAS/NKRAS

Chromosome

1p13.2, 12p12.1

Gene Symbol

KRAS/NKRAS

Test Detects

Mutation

Methodology

Category of Evidence

2A

Specimen Types

FFPE tumor tissue

Recommendation

…Determination of RAS mutations.

Test Purpose

Predictive

Guideline Page

COL 4 of 5, COL 4, COL 9

Note

All patients with metastatic colorectal cancer should be genotyped for RAS mutations. At the very least …

Figure 2. (Table) Example of PDF file generated from ‘‘print’’ command of National Comprehensive Cancer Network (NCCN) Biomarkers Compendium record. Reproduced with permission from the NCCN Biomarkers Compendium [1] 2014 National Comprehensive Cancer Network, Inc (NCCN.org; accessed February 21, 2014). To view the most recent and complete version of the NCCN Biomarkers Compendium, go online to NCCN.org. National Comprehensive Cancer Network, NCCN, NCCN Guidelines, and all other NCCN content are trademarks owned by the National Comprehensive Cancer Network, Inc.

Table 2. (List) Summary of Testing Types Included in the National Comprehensive Cancer Network Biomarkers Compendiuma,b

A large number of tests were grouped for the purposes of this simpliﬁed table into the category of gross chromosomal abnormalities. Interestingly, the guidelines so far contain only a single recommendation for the use of a gene expression proﬁling test, and this is the 21-gene reverse transcription–polymerase chain reaction test recommended within the breast cancer treatment guideline, where the score for this test can be used as part of a decision-making process for chemotherapy recommendations in node negative, hormone receptor–positive, HER2-negative disease.

Table 3 summarizes the biomarker tests included in the NCCN Biomarkers Compendium that are predictive for either responsiveness (eg, BRAF mutation and vemurafenib sensitivity) or nonresponsiveness (eg, KRAS mutation testing and cetuximab or panitumumab insensitivity) to a particular type of therapy. As the number of companion diagnostics and targeted therapies grows, we expect this category of test to become one of the largest categories of testing contained within the Biomarkers Compendium, and it may be surprising to note that only 15 of these types of test are currently recommended within the NCCN Guidelines.

The NCCN Biomarkers Compendium generally avoids recommendations for particular methodologies or test kits to use to assess mutations and translocations. The choice of methodology and supplier for carrying out the recommended biomarker tests remains that of the treating oncologists and pathologists.

The NCCN Biomarkers Compendium may be used by payers as a reference for coverage decisions and by clinicians as a guide to which biomarkers are appropriate to test. The Biomarkers Compendium focuses on the clinical usefulness of biomarker testing rather than speciﬁc tests or test kits that identify the presence or absence of the marker. Other groups are continuing to assess clinical and analytic validity for speciﬁc biomarker test methodologies. Even the US Food and Drug Administration approval process is limited to clinical and analytic validity, and does not speciﬁcally address clinical utility. The NCCN Biomarkers Compendium is complementary to these other efforts. By providing biomarker testing information, the NCCN Biomarkers Compendium aims to ensure that patients have coverage and access to appropriate biomarker testing, based on the evaluations and recommendations of the expert NCCN panel members.

Numerous crystal structures have been reported for the isolated extracellular region and tyrosine kinase domain of the epidermal growth factor receptor (EGFR) and its relatives, in different states of activation and bound to a variety of inhibitors used in cancer therapy. The next challenge is to put these structures together accurately in functional models of the intact receptor in its membrane environment. The intact EGFR has been studied using electron microscopy, chemical biology methods, biochemically, and computationally. The distinct approaches yield different impressions about the structural modes of communication between extracellular and intracellular regions. They highlight possible differences between ligands, and also underline the need to understand how the receptor interacts with the membrane itself.